The deal comes after incumbent carrier Virgin Australia said it would stop flying to Albany and Esperance from February 2016 because the services were not profitable.

"We're looking for an airline that's primary focus is on the development of air services in regional Western Australia and Rex has certainly come up the highest of anyone we have considered."

Transport Minister Dean Nalder

Mr Nalder said Rex was the right choice for the region.

"We're looking for an airline that's primary focus is on the development of air services in regional Western Australia and Rex has certainly come up the highest of anyone we have considered," he said.

However, there are concerns the increase in services will not make up for the lower capacity planes Rex plan to fly on the route.

The Member for Albany, Peter Watson, said he estimated about 16 people could miss out per flight.

"Most businessmen will want to go on the early flight, most people that are going up for PATS [the Patient Assisted Travel Scheme] will want to go on the early flight and most people who are travelling would go on the early flight," he said.

"So it depends on the schedule when the next flight is.

"The fact we've only got 32-seaters is a concern to me."

"Virgin was losing money operating here, so we don't obviously want to set a price that will cause us to lose money but we think we can at least match their very best prices and we hope to do better."

Rex Airlines' John Sharp

Rex deputy chairman John Sharp would not say if it would offer cheaper tickets than Virgin.

"Virgin was losing money operating here, so we don't obviously want to set a price that will cause us to lose money," he said.

"But we think we can at least match their very best prices and we hope to do better."

He said landing charges at Perth Airport were the highest the company had experienced in Australia.